plot,ReadCounts,missing-method

plot,RLEReadCounts,missing-method


	Object of class <code>ReadCounts</code> or <code>RLEReadCounts</code>. 



	Index or name of chromosome for which read counts should be plotted.



	For type &#145;window&#146;, the center coordinate of the window to plot.  


center


  	For type &#145;window&#146;, an object of type <code>BindScore</code> 
  	(or <code>BindScore</code>) that should be used to include information
  	about the score and predicted binding sites into the plot.


score


	For type &#145;window&#146;, the width of the window.  


width


	Character string indicating the type of plot that should be produced (see details).  


type


Produces plots to assess the distribution of reads, either for an entire chromosome or within
a (small) window.


hplot

ChIPseqR identifies protein binding sites from ChIP-seq
and nucleosome positioning experiments. The model used to
describe binding events was developed to locate nucleosomes but
should flexible enough to handle other types of experiments as
well.

Peter Humburg

ChIPseqR

Identifying Protein Binding Sites in High-Throughput Sequencing
Data

plot,ReadCounts,missing-method function

Object of class <code><linkS4class>ReadCounts</linkS4class></code> or <code><linkS4class>RLEReadCounts</linkS4class></code>.

Index or name of chromosome for which read counts should be plotted.

For type <sQuote>window</sQuote>, the center coordinate of the window to plot.

For type <sQuote>window</sQuote>, an object of type <code><linkS4class>BindScore</linkS4class></code> 
  	(or <code><linkS4class>BindScore</linkS4class></code>) that should be used to include information
  	about the score and predicted binding sites into the plot.

For type <sQuote>window</sQuote>, the width of the window.

Character string indicating the type of plot that should be produced (see details).

Produces plots to assess the distribution of reads, either for an entire chromosome or within
a (small) window.

plot,ReadCounts,missing-method: Diagnostic Plots for Read Counts

Description

Usage

Arguments

Value

Details

See Also